Starting phenix.real_space_refine on Tue Jul 7 00:39:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge5_51290/07_2026/9ge5_51290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge5_51290/07_2026/9ge5_51290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ge5_51290/07_2026/9ge5_51290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge5_51290/07_2026/9ge5_51290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ge5_51290/07_2026/9ge5_51290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge5_51290/07_2026/9ge5_51290.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 243 5.49 5 S 168 5.16 5 C 24450 2.51 5 N 7130 2.21 5 O 8025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 322 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40017 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3345 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3454 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "C" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3413 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 425} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3318 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Chain: "E" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3404 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 427} Chain: "F" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3377 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Chain: "G" Number of atoms: 5609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5609 Classifications: {'peptide': 682} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 653} Chain breaks: 3 Chain: "H" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 851 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "J" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3278 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 382} Chain breaks: 2 Chain: "K" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2334 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "L" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 2299 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "M" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "Q" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 767 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "R" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "T" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.10, per 1000 atoms: 0.18 Number of scatterers: 40017 At special positions: 0 Unit cell: (135.222, 188.293, 187.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 168 16.00 P 243 15.00 O 8025 8.00 N 7130 7.00 C 24450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8308 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 34 sheets defined 48.9% alpha, 10.6% beta 98 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 3.598A pdb=" N ALA A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.828A pdb=" N ALA A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.726A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 272 through 289 removed outlier: 4.073A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.068A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.960A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.580A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 450 through 454 removed outlier: 4.229A pdb=" N TYR A 454 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 4.318A pdb=" N ALA B 48 " --> pdb=" O ASN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.564A pdb=" N GLY B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.660A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.510A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.505A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.560A pdb=" N ALA B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 272 through 289 removed outlier: 3.620A pdb=" N ARG B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.671A pdb=" N MET B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 4.219A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 320 " --> pdb=" O HIS B 316 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.632A pdb=" N GLY B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.904A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.571A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.759A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 Processing helix chain 'B' and resid 451 through 454 removed outlier: 3.818A pdb=" N TYR B 454 " --> pdb=" O GLN B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.574A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.908A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 174 through 180 removed outlier: 4.330A pdb=" N GLU C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.768A pdb=" N GLN C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 319 removed outlier: 4.574A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.639A pdb=" N THR C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.519A pdb=" N HIS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.692A pdb=" N ILE C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 454 removed outlier: 4.360A pdb=" N TYR C 454 " --> pdb=" O GLN C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 454' Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.667A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.574A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 244 through 253 removed outlier: 4.302A pdb=" N ARG D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.596A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.626A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.038A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 379 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 399 through 416 removed outlier: 4.383A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 444 Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 106 through 109 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 175 through 185 removed outlier: 3.688A pdb=" N GLU E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 214 Processing helix chain 'E' and resid 244 through 253 removed outlier: 4.112A pdb=" N ARG E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 269 through 286 removed outlier: 3.692A pdb=" N ARG E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 4.077A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.726A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 443 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.694A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 257 through 263 removed outlier: 4.115A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 removed outlier: 3.652A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.749A pdb=" N MET F 303 " --> pdb=" O GLU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.635A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.503A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 379 removed outlier: 3.891A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.763A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 445 removed outlier: 3.956A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 450 Processing helix chain 'G' and resid 519 through 536 Processing helix chain 'G' and resid 550 through 559 removed outlier: 3.610A pdb=" N ALA G 555 " --> pdb=" O VAL G 551 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU G 556 " --> pdb=" O GLN G 552 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA G 558 " --> pdb=" O ILE G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 568 removed outlier: 3.838A pdb=" N TRP G 567 " --> pdb=" O ARG G 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 579 Processing helix chain 'G' and resid 580 through 585 Processing helix chain 'G' and resid 586 through 588 No H-bonds generated for 'chain 'G' and resid 586 through 588' Processing helix chain 'G' and resid 601 through 606 Processing helix chain 'G' and resid 608 through 613 removed outlier: 3.533A pdb=" N SER G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 642 removed outlier: 4.239A pdb=" N GLN G 636 " --> pdb=" O GLN G 632 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS G 639 " --> pdb=" O VAL G 635 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR G 640 " --> pdb=" O GLN G 636 " (cutoff:3.500A) Processing helix chain 'G' and resid 654 through 658 Processing helix chain 'G' and resid 662 through 669 Processing helix chain 'G' and resid 687 through 690 Processing helix chain 'G' and resid 691 through 699 removed outlier: 3.761A pdb=" N LEU G 695 " --> pdb=" O LEU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 710 removed outlier: 4.178A pdb=" N PHE G 709 " --> pdb=" O SER G 705 " (cutoff:3.500A) Processing helix chain 'G' and resid 730 through 740 Processing helix chain 'G' and resid 748 through 753 Processing helix chain 'G' and resid 770 through 780 removed outlier: 3.851A pdb=" N LEU G 774 " --> pdb=" O ARG G 770 " (cutoff:3.500A) Processing helix chain 'G' and resid 809 through 818 removed outlier: 4.031A pdb=" N VAL G 815 " --> pdb=" O GLN G 811 " (cutoff:3.500A) Processing helix chain 'G' and resid 819 through 822 Processing helix chain 'G' and resid 841 through 848 Processing helix chain 'G' and resid 849 through 854 removed outlier: 3.550A pdb=" N ASN G 854 " --> pdb=" O ILE G 850 " (cutoff:3.500A) Processing helix chain 'G' and resid 854 through 864 removed outlier: 4.300A pdb=" N TRP G 860 " --> pdb=" O SER G 856 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 861 " --> pdb=" O ARG G 857 " (cutoff:3.500A) Processing helix chain 'G' and resid 868 through 877 Processing helix chain 'G' and resid 888 through 893 Processing helix chain 'G' and resid 897 through 907 Processing helix chain 'G' and resid 908 through 932 removed outlier: 3.560A pdb=" N LYS G 921 " --> pdb=" O PHE G 917 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG G 925 " --> pdb=" O LYS G 921 " (cutoff:3.500A) Processing helix chain 'G' and resid 958 through 965 Processing helix chain 'G' and resid 967 through 972 removed outlier: 3.877A pdb=" N LEU G 971 " --> pdb=" O LEU G 967 " (cutoff:3.500A) Processing helix chain 'G' and resid 1028 through 1041 removed outlier: 3.912A pdb=" N TYR G1033 " --> pdb=" O ARG G1029 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G1034 " --> pdb=" O SER G1030 " (cutoff:3.500A) Processing helix chain 'G' and resid 1043 through 1053 Processing helix chain 'G' and resid 1054 through 1062 Processing helix chain 'G' and resid 1063 through 1067 Processing helix chain 'G' and resid 1075 through 1079 Processing helix chain 'G' and resid 1094 through 1100 removed outlier: 3.857A pdb=" N SER G1100 " --> pdb=" O LEU G1096 " (cutoff:3.500A) Processing helix chain 'G' and resid 1100 through 1117 Processing helix chain 'G' and resid 1126 through 1140 Processing helix chain 'G' and resid 1154 through 1164 removed outlier: 4.001A pdb=" N ASP G1158 " --> pdb=" O SER G1154 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET G1159 " --> pdb=" O GLU G1155 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G1160 " --> pdb=" O ARG G1156 " (cutoff:3.500A) Processing helix chain 'G' and resid 1201 through 1208 Processing helix chain 'G' and resid 1231 through 1248 removed outlier: 3.575A pdb=" N LEU G1235 " --> pdb=" O GLU G1231 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU G1243 " --> pdb=" O LYS G1239 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE G1244 " --> pdb=" O GLU G1240 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 235 removed outlier: 4.168A pdb=" N LEU H 213 " --> pdb=" O THR H 209 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG H 216 " --> pdb=" O MET H 212 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG H 219 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU H 233 " --> pdb=" O ARG H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 340 Processing helix chain 'I' and resid 143 through 151 Processing helix chain 'I' and resid 152 through 154 No H-bonds generated for 'chain 'I' and resid 152 through 154' Processing helix chain 'I' and resid 162 through 166 removed outlier: 3.890A pdb=" N ILE I 166 " --> pdb=" O TYR I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 207 removed outlier: 3.583A pdb=" N ARG I 207 " --> pdb=" O PHE I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 220 removed outlier: 3.824A pdb=" N GLY I 216 " --> pdb=" O ASP I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 121 Processing helix chain 'J' and resid 141 through 155 Processing helix chain 'J' and resid 165 through 175 Processing helix chain 'J' and resid 214 through 230 Processing helix chain 'J' and resid 238 through 249 removed outlier: 4.715A pdb=" N GLU J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE J 245 " --> pdb=" O ARG J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 263 Processing helix chain 'J' and resid 265 through 273 removed outlier: 3.978A pdb=" N ASN J 271 " --> pdb=" O ASP J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 454 removed outlier: 3.526A pdb=" N ALA J 451 " --> pdb=" O GLU J 447 " (cutoff:3.500A) Proline residue: J 452 - end of helix Processing helix chain 'J' and resid 455 through 456 No H-bonds generated for 'chain 'J' and resid 455 through 456' Processing helix chain 'J' and resid 457 through 461 Processing helix chain 'J' and resid 466 through 477 removed outlier: 4.081A pdb=" N GLU J 470 " --> pdb=" O ALA J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 489 removed outlier: 3.671A pdb=" N GLN J 489 " --> pdb=" O GLU J 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 500 Processing helix chain 'J' and resid 502 through 513 removed outlier: 3.686A pdb=" N LYS J 509 " --> pdb=" O ALA J 505 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 544 Processing helix chain 'J' and resid 554 through 558 Processing helix chain 'M' and resid 46 through 57 removed outlier: 3.816A pdb=" N GLU M 50 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 79 Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 132 removed outlier: 3.673A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG M 131 " --> pdb=" O ALA M 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 77 removed outlier: 4.640A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.551A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 52 removed outlier: 4.234A pdb=" N ILE Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.194A pdb=" N ARG Q 72 " --> pdb=" O GLN Q 68 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE Q 74 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.703A pdb=" N ALA Q 91 " --> pdb=" O SER Q 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN Q 93 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU Q 94 " --> pdb=" O MET Q 90 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU Q 109 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 4.157A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG Q 129 " --> pdb=" O GLN Q 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 removed outlier: 3.599A pdb=" N GLY R 28 " --> pdb=" O ASN R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.592A pdb=" N HIS R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 76 " --> pdb=" O TYR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 removed outlier: 4.114A pdb=" N ARG S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 37 removed outlier: 3.726A pdb=" N ARG S 35 " --> pdb=" O HIS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 73 removed outlier: 3.619A pdb=" N LEU S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 89 Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 46 removed outlier: 4.123A pdb=" N LYS T 46 " --> pdb=" O TYR T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 84 removed outlier: 3.600A pdb=" N ASN T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 102 removed outlier: 3.550A pdb=" N ILE T 94 " --> pdb=" O THR T 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG T 99 " --> pdb=" O GLN T 95 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.423A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 141 removed outlier: 5.637A pdb=" N VAL A 135 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS A 162 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 137 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS A 156 " --> pdb=" O CYS A 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 172 current: chain 'A' and resid 200 through 206 removed outlier: 6.072A pdb=" N VAL A 221 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG A 205 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.501A pdb=" N ILE B 3 " --> pdb=" O LEU G 762 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N TYR G 764 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU B 5 " --> pdb=" O TYR G 764 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU G1121 " --> pdb=" O ILE G1192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 97 removed outlier: 7.027A pdb=" N ALA B 65 " --> pdb=" O MET B 359 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE B 361 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU B 67 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 143 removed outlier: 5.668A pdb=" N VAL B 135 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 162 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR B 143 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE B 154 " --> pdb=" O THR B 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 172 current: chain 'B' and resid 200 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 437 through 438 removed outlier: 6.802A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 73 " --> pdb=" O MET E 326 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR E 328 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE E 75 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.187A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 65 " --> pdb=" O MET C 359 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE C 361 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 67 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 142 removed outlier: 5.742A pdb=" N VAL C 135 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS C 162 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C 137 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 156 " --> pdb=" O CYS C 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 172 current: chain 'C' and resid 200 through 205 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 200 through 205 current: chain 'E' and resid 158 through 164 removed outlier: 4.356A pdb=" N GLY E 159 " --> pdb=" O LEU E 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 174 current: chain 'E' and resid 204 through 207 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 204 through 207 current: chain 'G' and resid 996 through 1005 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 996 through 1005 current: chain 'H' and resid 281 through 286 Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.680A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 296 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA D 327 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE D 298 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 147 removed outlier: 6.812A pdb=" N THR D 162 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE D 145 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS D 160 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 174 current: chain 'D' and resid 202 through 208 removed outlier: 6.209A pdb=" N VAL D 225 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG D 207 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AB7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'E' and resid 333 through 334 Processing sheet with id=AB9, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC1, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.459A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 148 removed outlier: 5.362A pdb=" N VAL F 142 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS F 164 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU F 144 " --> pdb=" O THR F 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 168 through 172 current: chain 'F' and resid 201 through 208 removed outlier: 6.209A pdb=" N VAL F 225 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG F 207 " --> pdb=" O VAL F 225 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 224 through 225 current: chain 'H' and resid 328 through 329 Processing sheet with id=AC3, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AC4, first strand: chain 'G' and resid 539 through 540 removed outlier: 6.647A pdb=" N GLY G 539 " --> pdb=" O LEU G 678 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET G 649 " --> pdb=" O LEU G 677 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU G 679 " --> pdb=" O MET G 649 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G 571 " --> pdb=" O VAL G 650 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP G 652 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE G 573 " --> pdb=" O ASP G 652 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 831 through 833 removed outlier: 6.377A pdb=" N PHE G 831 " --> pdb=" O THR G1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AC7, first strand: chain 'J' and resid 58 through 62 removed outlier: 4.125A pdb=" N GLN J 60 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL J 42 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY J 164 " --> pdb=" O LEU J 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AC9, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AD1, first strand: chain 'J' and resid 183 through 188 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 202 through 203 current: chain 'J' and resid 523 through 525 Processing sheet with id=AD2, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.960A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AD4, first strand: chain 'N' and resid 96 through 97 removed outlier: 6.937A pdb=" N THR N 96 " --> pdb=" O THR S 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.708A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.863A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'S' and resid 77 through 78 1446 hydrogen bonds defined for protein. 4119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 250 hydrogen bonds 500 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 9.99 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.57: 40406 1.57 - 1.94: 745 1.94 - 2.30: 4 2.30 - 2.67: 0 2.67 - 3.03: 1 Bond restraints: 41156 Sorted by residual: bond pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " ideal model delta sigma weight residual 1.530 3.033 -1.503 1.68e-02 3.54e+03 8.00e+03 bond pdb=" C3' DG K 3 " pdb=" C2' DG K 3 " ideal model delta sigma weight residual 1.516 1.998 -0.482 8.00e-03 1.56e+04 3.63e+03 bond pdb=" C2' DG K 3 " pdb=" C1' DG K 3 " ideal model delta sigma weight residual 1.518 2.024 -0.506 1.00e-02 1.00e+04 2.56e+03 bond pdb=" C4' DG K 3 " pdb=" C3' DG K 3 " ideal model delta sigma weight residual 1.529 2.018 -0.489 1.00e-02 1.00e+04 2.39e+03 bond pdb=" C4' DG K 3 " pdb=" O4' DG K 3 " ideal model delta sigma weight residual 1.446 1.920 -0.474 1.00e-02 1.00e+04 2.24e+03 ... (remaining 41151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 54613 4.08 - 8.16: 1871 8.16 - 12.23: 38 12.23 - 16.31: 17 16.31 - 20.39: 5 Bond angle restraints: 56544 Sorted by residual: angle pdb=" O4' DG K 3 " pdb=" C1' DG K 3 " pdb=" N9 DG K 3 " ideal model delta sigma weight residual 108.00 123.34 -15.34 7.00e-01 2.04e+00 4.80e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.11 19.76 1.00e+00 1.00e+00 3.91e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 118.83 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" O5' DC L 34 " pdb=" C5' DC L 34 " pdb=" C4' DC L 34 " ideal model delta sigma weight residual 109.40 120.96 -11.56 8.00e-01 1.56e+00 2.09e+02 angle pdb=" N LYS I 136 " pdb=" CA LYS I 136 " pdb=" C LYS I 136 " ideal model delta sigma weight residual 112.89 95.39 17.50 1.24e+00 6.50e-01 1.99e+02 ... (remaining 56539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 23284 35.30 - 70.60: 1187 70.60 - 105.90: 84 105.90 - 141.20: 7 141.20 - 176.50: 7 Dihedral angle restraints: 24569 sinusoidal: 11688 harmonic: 12881 Sorted by residual: dihedral pdb=" N LYS I 136 " pdb=" C LYS I 136 " pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " ideal model delta harmonic sigma weight residual 122.80 142.94 -20.14 0 2.50e+00 1.60e-01 6.49e+01 dihedral pdb=" C LYS I 136 " pdb=" N LYS I 136 " pdb=" CA LYS I 136 " pdb=" CB LYS I 136 " ideal model delta harmonic sigma weight residual -122.60 -141.24 18.64 0 2.50e+00 1.60e-01 5.56e+01 dihedral pdb=" C5' ADP J 701 " pdb=" O5' ADP J 701 " pdb=" PA ADP J 701 " pdb=" O2A ADP J 701 " ideal model delta sinusoidal sigma weight residual 300.00 151.61 148.39 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 24566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 6358 0.274 - 0.547: 57 0.547 - 0.821: 1 0.821 - 1.095: 0 1.095 - 1.368: 3 Chirality restraints: 6419 Sorted by residual: chirality pdb=" CA LYS I 136 " pdb=" N LYS I 136 " pdb=" C LYS I 136 " pdb=" CB LYS I 136 " both_signs ideal model delta sigma weight residual False 2.51 3.88 -1.37 2.00e-01 2.50e+01 4.68e+01 chirality pdb=" C3' DG K 3 " pdb=" C4' DG K 3 " pdb=" O3' DG K 3 " pdb=" C2' DG K 3 " both_signs ideal model delta sigma weight residual False -2.73 -4.05 1.32 2.00e-01 2.50e+01 4.38e+01 chirality pdb=" C4' DG K 3 " pdb=" C5' DG K 3 " pdb=" O4' DG K 3 " pdb=" C3' DG K 3 " both_signs ideal model delta sigma weight residual False -2.53 -3.69 1.16 2.00e-01 2.50e+01 3.35e+01 ... (remaining 6416 not shown) Planarity restraints: 6443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG K -29 " 0.055 2.00e-02 2.50e+03 1.33e-01 5.28e+02 pdb=" N9 DG K -29 " 0.069 2.00e-02 2.50e+03 pdb=" C8 DG K -29 " -0.178 2.00e-02 2.50e+03 pdb=" N7 DG K -29 " -0.195 2.00e-02 2.50e+03 pdb=" C5 DG K -29 " 0.041 2.00e-02 2.50e+03 pdb=" C6 DG K -29 " 0.101 2.00e-02 2.50e+03 pdb=" O6 DG K -29 " 0.071 2.00e-02 2.50e+03 pdb=" N1 DG K -29 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DG K -29 " 0.023 2.00e-02 2.50e+03 pdb=" N2 DG K -29 " -0.279 2.00e-02 2.50e+03 pdb=" N3 DG K -29 " 0.152 2.00e-02 2.50e+03 pdb=" C4 DG K -29 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 32 " -0.323 2.00e-02 2.50e+03 1.32e-01 5.24e+02 pdb=" N9 DG K 32 " 0.042 2.00e-02 2.50e+03 pdb=" C8 DG K 32 " 0.149 2.00e-02 2.50e+03 pdb=" N7 DG K 32 " 0.118 2.00e-02 2.50e+03 pdb=" C5 DG K 32 " 0.054 2.00e-02 2.50e+03 pdb=" C6 DG K 32 " -0.055 2.00e-02 2.50e+03 pdb=" O6 DG K 32 " -0.202 2.00e-02 2.50e+03 pdb=" N1 DG K 32 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DG K 32 " 0.039 2.00e-02 2.50e+03 pdb=" N2 DG K 32 " 0.080 2.00e-02 2.50e+03 pdb=" N3 DG K 32 " 0.066 2.00e-02 2.50e+03 pdb=" C4 DG K 32 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG L -56 " 0.300 2.00e-02 2.50e+03 1.28e-01 4.94e+02 pdb=" N9 DG L -56 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG L -56 " -0.137 2.00e-02 2.50e+03 pdb=" N7 DG L -56 " -0.122 2.00e-02 2.50e+03 pdb=" C5 DG L -56 " -0.058 2.00e-02 2.50e+03 pdb=" C6 DG L -56 " 0.045 2.00e-02 2.50e+03 pdb=" O6 DG L -56 " 0.233 2.00e-02 2.50e+03 pdb=" N1 DG L -56 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DG L -56 " -0.056 2.00e-02 2.50e+03 pdb=" N2 DG L -56 " -0.042 2.00e-02 2.50e+03 pdb=" N3 DG L -56 " -0.057 2.00e-02 2.50e+03 pdb=" C4 DG L -56 " -0.072 2.00e-02 2.50e+03 ... (remaining 6440 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 742 2.71 - 3.26: 39271 3.26 - 3.81: 63023 3.81 - 4.35: 86414 4.35 - 4.90: 134871 Nonbonded interactions: 324321 Sorted by model distance: nonbonded pdb=" CA LYS I 136 " pdb=" O4' DG K 3 " model vdw 2.167 3.470 nonbonded pdb=" CB LYS I 136 " pdb=" O4' DG K 3 " model vdw 2.192 3.440 nonbonded pdb=" CA LYS I 136 " pdb=" C1' DG K 3 " model vdw 2.259 3.900 nonbonded pdb=" CB LYS I 136 " pdb=" C1' DG K 3 " model vdw 2.268 3.870 nonbonded pdb=" CA LYS I 136 " pdb=" C2' DG K 3 " model vdw 2.273 3.870 ... (remaining 324316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 141 or resid 152 through 454)) selection = (chain 'B' and (resid 12 through 141 or resid 152 through 454)) selection = (chain 'C' and (resid 12 through 141 or resid 152 through 454)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) selection = (chain 'F' and (resid 15 through 149 or resid 156 through 214 or resid 222 throu \ gh 501)) } ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 43 through 133) } ncs_group { reference = (chain 'N' and resid 25 through 102) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 37.050 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 44.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.503 41156 Z= 1.167 Angle : 1.886 20.388 56544 Z= 1.460 Chirality : 0.099 1.368 6419 Planarity : 0.019 0.240 6443 Dihedral : 18.962 176.501 16261 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.87 % Favored : 95.56 % Rotamer: Outliers : 1.15 % Allowed : 4.90 % Favored : 93.94 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.11), residues: 4415 helix: -1.75 (0.09), residues: 1942 sheet: 0.14 (0.19), residues: 629 loop : -0.80 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG J 43 TYR 0.191 0.023 TYR S 57 PHE 0.058 0.011 PHE G1193 TRP 0.172 0.023 TRP J 540 HIS 0.016 0.004 HIS J 119 Details of bonding type rmsd/Z covalent geometry : bond 0.01574 / 1.17 (41156) covalent geometry : angle 1.88574 / 1.46 (56544) hydrogen bonds : bond 0.16366 / 11.08 ( 1696) hydrogen bonds : angle 7.54402 / 5.34 ( 4619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 999 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9112 (p) REVERT: A 61 MET cc_start: 0.7919 (mmm) cc_final: 0.7666 (mmm) REVERT: A 90 LYS cc_start: 0.8521 (mppt) cc_final: 0.8024 (tptt) REVERT: A 183 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7753 (tp30) REVERT: A 259 MET cc_start: 0.7313 (ptm) cc_final: 0.7097 (tpp) REVERT: A 449 ASP cc_start: 0.9513 (m-30) cc_final: 0.9271 (m-30) REVERT: B 5 GLU cc_start: 0.6634 (mt-10) cc_final: 0.5920 (mt-10) REVERT: B 100 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7699 (tp30) REVERT: B 134 GLU cc_start: 0.7928 (tt0) cc_final: 0.7661 (tm-30) REVERT: B 168 LYS cc_start: 0.8347 (mttp) cc_final: 0.8071 (mtpt) REVERT: B 335 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8422 (t0) REVERT: B 371 MET cc_start: 0.8730 (mmt) cc_final: 0.8500 (mtt) REVERT: C 40 VAL cc_start: 0.8719 (p) cc_final: 0.8500 (m) REVERT: C 106 ILE cc_start: 0.8735 (tt) cc_final: 0.8457 (pt) REVERT: C 165 LYS cc_start: 0.8861 (tttp) cc_final: 0.8562 (mptt) REVERT: C 190 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7504 (t) REVERT: C 192 TYR cc_start: 0.8930 (p90) cc_final: 0.8497 (p90) REVERT: C 268 LYS cc_start: 0.8192 (mttt) cc_final: 0.7941 (mttm) REVERT: C 363 THR cc_start: 0.9293 (m) cc_final: 0.8917 (p) REVERT: D 134 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8970 (mm-30) REVERT: D 146 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7589 (pt0) REVERT: D 149 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7127 (ppt170) REVERT: D 235 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.8234 (ttp80) REVERT: D 447 GLN cc_start: 0.8496 (tt0) cc_final: 0.8099 (tp-100) REVERT: E 47 VAL cc_start: 0.8677 (m) cc_final: 0.8206 (p) REVERT: E 88 MET cc_start: 0.8720 (mmp) cc_final: 0.8478 (mmm) REVERT: E 124 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8013 (mtp85) REVERT: E 215 TYR cc_start: 0.6930 (t80) cc_final: 0.6571 (t80) REVERT: E 353 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8296 (ttm170) REVERT: E 446 TYR cc_start: 0.8127 (m-10) cc_final: 0.7869 (m-10) REVERT: F 34 ASP cc_start: 0.8160 (m-30) cc_final: 0.7741 (p0) REVERT: F 88 MET cc_start: 0.8214 (mmp) cc_final: 0.7997 (mmm) REVERT: F 112 GLU cc_start: 0.8672 (pt0) cc_final: 0.8396 (pp20) REVERT: F 116 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7499 (p) REVERT: F 172 TYR cc_start: 0.8688 (m-80) cc_final: 0.8471 (m-80) REVERT: F 248 ASP cc_start: 0.8139 (m-30) cc_final: 0.7732 (m-30) REVERT: F 274 GLU cc_start: 0.8697 (pt0) cc_final: 0.8475 (tm-30) REVERT: G 573 ILE cc_start: 0.8349 (mp) cc_final: 0.7987 (mt) REVERT: G 593 PHE cc_start: 0.6980 (m-80) cc_final: 0.6571 (m-80) REVERT: G 599 TRP cc_start: 0.8879 (p-90) cc_final: 0.7927 (p90) REVERT: G 646 TRP cc_start: 0.8014 (m100) cc_final: 0.7276 (m-90) REVERT: G 649 MET cc_start: 0.5524 (mmm) cc_final: 0.5204 (mmm) REVERT: G 688 MET cc_start: 0.7278 (mmm) cc_final: 0.7036 (mmm) REVERT: G 765 CYS cc_start: 0.7445 (m) cc_final: 0.7155 (p) REVERT: G 770 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8438 (ttt180) REVERT: G 810 MET cc_start: 0.8549 (mmm) cc_final: 0.8131 (mmt) REVERT: G 821 LEU cc_start: 0.9029 (mt) cc_final: 0.8790 (mt) REVERT: G 856 SER cc_start: 0.9189 (p) cc_final: 0.8978 (t) REVERT: G 880 LYS cc_start: 0.8848 (mttt) cc_final: 0.8599 (mmtt) REVERT: G 1123 TYR cc_start: 0.6693 (m-80) cc_final: 0.6403 (m-80) REVERT: G 1129 MET cc_start: 0.8956 (tpp) cc_final: 0.8718 (tpt) REVERT: G 1144 TYR cc_start: 0.8277 (p90) cc_final: 0.8025 (p90) REVERT: G 1145 MET cc_start: 0.8186 (mtt) cc_final: 0.7953 (mtm) REVERT: G 1216 THR cc_start: 0.8375 (p) cc_final: 0.8103 (t) REVERT: I 120 LYS cc_start: 0.8586 (mttt) cc_final: 0.8383 (tptt) REVERT: I 146 GLN cc_start: 0.8934 (mp10) cc_final: 0.8653 (mp10) REVERT: I 159 ASN cc_start: 0.6013 (m-40) cc_final: 0.5630 (p0) REVERT: I 192 GLN cc_start: 0.8521 (mt0) cc_final: 0.8268 (mt0) REVERT: I 208 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8004 (ptt180) REVERT: I 220 LEU cc_start: 0.9255 (tp) cc_final: 0.9028 (tt) REVERT: J 12 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7999 (tmt170) REVERT: J 36 ASP cc_start: 0.9039 (m-30) cc_final: 0.8698 (t0) REVERT: J 93 MET cc_start: 0.3359 (tpt) cc_final: 0.2635 (tpt) REVERT: J 132 ILE cc_start: 0.8967 (pt) cc_final: 0.8632 (tt) REVERT: J 133 VAL cc_start: 0.8905 (p) cc_final: 0.8598 (m) REVERT: J 163 TYR cc_start: 0.7589 (m-80) cc_final: 0.7166 (m-10) REVERT: J 242 MET cc_start: 0.7946 (mmp) cc_final: 0.7687 (mmp) REVERT: J 475 ILE cc_start: 0.9156 (pt) cc_final: 0.8839 (mt) REVERT: J 540 TRP cc_start: 0.8800 (t60) cc_final: 0.8442 (t60) REVERT: J 555 LYS cc_start: 0.9099 (pttt) cc_final: 0.8856 (mmmm) REVERT: M 50 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7294 (mp0) REVERT: M 61 LEU cc_start: 0.7380 (mt) cc_final: 0.7154 (mt) REVERT: M 67 PHE cc_start: 0.8575 (t80) cc_final: 0.7985 (t80) REVERT: M 99 TYR cc_start: 0.7852 (t80) cc_final: 0.7353 (t80) REVERT: N 88 TYR cc_start: 0.7159 (m-10) cc_final: 0.6774 (m-80) REVERT: Q 67 PHE cc_start: 0.7277 (t80) cc_final: 0.7018 (t80) REVERT: Q 104 PHE cc_start: 0.7464 (m-80) cc_final: 0.7253 (m-10) REVERT: Q 122 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7792 (ptmt) REVERT: Q 134 ARG cc_start: 0.6958 (ttm170) cc_final: 0.6644 (ttm-80) REVERT: R 32 PRO cc_start: 0.5508 (Cg_endo) cc_final: 0.4968 (Cg_exo) REVERT: R 49 LEU cc_start: 0.7404 (mp) cc_final: 0.6746 (mt) REVERT: R 58 LEU cc_start: 0.8565 (tp) cc_final: 0.8264 (tp) REVERT: R 75 HIS cc_start: 0.7025 (t70) cc_final: 0.6688 (t-170) REVERT: S 91 GLU cc_start: 0.8713 (pm20) cc_final: 0.8478 (pp20) REVERT: T 44 VAL cc_start: 0.8357 (t) cc_final: 0.8109 (p) REVERT: T 92 ARG cc_start: 0.7473 (ptm160) cc_final: 0.7140 (ptt-90) REVERT: T 113 GLU cc_start: 0.8089 (tp30) cc_final: 0.7337 (tp30) outliers start: 44 outliers final: 11 residues processed: 1035 average time/residue: 0.2760 time to fit residues: 443.9151 Evaluate side-chains 601 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 586 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain J residue 487 LEU Chi-restraints excluded: chain T residue 33 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 247 ASN B 247 ASN B 262 GLN E 146 GLN E 221 GLN E 233 GLN E 240 HIS F 240 HIS G 832 HIS G 873 GLN G1184 ASN H 226 GLN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 GLN R 25 ASN R 64 ASN S 24 GLN S 73 ASN T 67 ASN T 109 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086273 restraints weight = 94838.771| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.86 r_work: 0.3231 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.272 41156 Z= 0.192 Angle : 0.854 24.418 56544 Z= 0.453 Chirality : 0.054 0.297 6419 Planarity : 0.005 0.064 6443 Dihedral : 21.396 176.515 7488 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 3.04 % Allowed : 11.59 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.12), residues: 4415 helix: -0.54 (0.11), residues: 1964 sheet: -0.22 (0.19), residues: 653 loop : -0.56 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 67 TYR 0.023 0.002 TYR G 533 PHE 0.038 0.002 PHE G 641 TRP 0.018 0.002 TRP G 665 HIS 0.012 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (41156) covalent geometry : angle 0.85415 / 0.45 (56544) hydrogen bonds : bond 0.06135 / 4.09 ( 1696) hydrogen bonds : angle 5.18049 / 3.70 ( 4619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 632 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8811 (mtpt) REVERT: A 432 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8485 (tp30) REVERT: B 181 GLN cc_start: 0.9072 (mt0) cc_final: 0.8843 (pt0) REVERT: B 405 TYR cc_start: 0.8830 (t80) cc_final: 0.8506 (t80) REVERT: C 105 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8379 (mt-10) REVERT: C 363 THR cc_start: 0.9427 (m) cc_final: 0.9174 (p) REVERT: C 418 LYS cc_start: 0.9025 (mptt) cc_final: 0.8820 (mptt) REVERT: D 267 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8240 (mm-30) REVERT: E 46 MET cc_start: 0.7600 (mtp) cc_final: 0.7105 (mtp) REVERT: E 88 MET cc_start: 0.8822 (mmp) cc_final: 0.8245 (mmm) REVERT: E 103 ILE cc_start: 0.8716 (mm) cc_final: 0.8484 (mt) REVERT: E 168 MET cc_start: 0.7765 (mmm) cc_final: 0.7326 (mpp) REVERT: E 441 GLN cc_start: 0.8338 (tp40) cc_final: 0.8121 (tp40) REVERT: F 34 ASP cc_start: 0.8118 (m-30) cc_final: 0.7780 (p0) REVERT: F 248 ASP cc_start: 0.8259 (m-30) cc_final: 0.7992 (m-30) REVERT: F 442 TYR cc_start: 0.8569 (m-10) cc_final: 0.8252 (m-10) REVERT: G 593 PHE cc_start: 0.7523 (m-80) cc_final: 0.6983 (m-80) REVERT: G 641 PHE cc_start: 0.7412 (m-80) cc_final: 0.6877 (m-80) REVERT: G 646 TRP cc_start: 0.7018 (m100) cc_final: 0.6802 (m100) REVERT: G 770 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7736 (ttt180) REVERT: G 821 LEU cc_start: 0.8861 (mt) cc_final: 0.8644 (mt) REVERT: G 880 LYS cc_start: 0.8451 (mttt) cc_final: 0.8167 (mmtt) REVERT: G 1123 TYR cc_start: 0.8031 (m-80) cc_final: 0.7527 (m-80) REVERT: H 272 MET cc_start: 0.8643 (mmt) cc_final: 0.7903 (mmm) REVERT: I 139 ARG cc_start: 0.4185 (mtt180) cc_final: 0.2859 (tpm170) REVERT: I 140 THR cc_start: 0.7264 (t) cc_final: 0.6853 (t) REVERT: I 146 GLN cc_start: 0.8156 (mp10) cc_final: 0.7883 (mp10) REVERT: I 172 PHE cc_start: 0.8201 (m-80) cc_final: 0.7565 (m-80) REVERT: I 206 ILE cc_start: 0.8840 (mt) cc_final: 0.8613 (mt) REVERT: I 208 ARG cc_start: 0.8619 (mtm110) cc_final: 0.7981 (ptt180) REVERT: J 93 MET cc_start: 0.3337 (tpt) cc_final: 0.3128 (tpt) REVERT: J 148 MET cc_start: 0.8797 (tpp) cc_final: 0.8537 (tpp) REVERT: J 152 LEU cc_start: 0.9234 (mt) cc_final: 0.8950 (mt) REVERT: J 163 TYR cc_start: 0.6160 (m-80) cc_final: 0.5949 (m-10) REVERT: J 254 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8019 (mp0) REVERT: J 475 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9130 (mt) REVERT: J 497 ASN cc_start: 0.8731 (m110) cc_final: 0.8412 (m-40) REVERT: J 540 TRP cc_start: 0.9001 (t60) cc_final: 0.8798 (t60) REVERT: M 50 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8054 (mp0) REVERT: M 67 PHE cc_start: 0.8654 (t80) cc_final: 0.8325 (t80) REVERT: M 117 VAL cc_start: 0.6506 (m) cc_final: 0.5801 (p) REVERT: M 123 ASP cc_start: 0.7264 (m-30) cc_final: 0.6418 (t0) REVERT: N 72 TYR cc_start: 0.6584 (m-80) cc_final: 0.6352 (m-80) REVERT: N 88 TYR cc_start: 0.7102 (m-10) cc_final: 0.6901 (m-80) REVERT: Q 68 GLN cc_start: 0.8014 (tp40) cc_final: 0.7579 (mm-40) REVERT: Q 134 ARG cc_start: 0.6392 (ttm170) cc_final: 0.5861 (ttm110) REVERT: R 49 LEU cc_start: 0.7284 (mp) cc_final: 0.7073 (mt) REVERT: R 72 TYR cc_start: 0.7401 (m-80) cc_final: 0.6925 (m-80) REVERT: R 75 HIS cc_start: 0.7666 (t70) cc_final: 0.6896 (t-170) REVERT: R 88 TYR cc_start: 0.7843 (m-80) cc_final: 0.7526 (m-80) REVERT: S 57 TYR cc_start: 0.5407 (t80) cc_final: 0.5172 (t80) REVERT: S 87 ILE cc_start: 0.9005 (mt) cc_final: 0.8718 (mt) REVERT: S 92 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5603 (tp30) REVERT: S 94 ASN cc_start: 0.8525 (t0) cc_final: 0.8301 (m-40) REVERT: T 76 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8115 (pt0) REVERT: T 92 ARG cc_start: 0.7488 (ptm160) cc_final: 0.6876 (ptt-90) REVERT: T 93 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6628 (mt-10) REVERT: T 100 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.3924 (mm) REVERT: T 113 GLU cc_start: 0.8119 (tp30) cc_final: 0.7661 (tp30) outliers start: 116 outliers final: 63 residues processed: 703 average time/residue: 0.2528 time to fit residues: 285.5461 Evaluate side-chains 566 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 500 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain G residue 533 TYR Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 675 ASN Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 809 VAL Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1109 LEU Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain H residue 222 LYS Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 527 SER Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 92 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 11 optimal weight: 4.9990 chunk 320 optimal weight: 30.0000 chunk 317 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 chunk 429 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 89 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 65 optimal weight: 0.0020 chunk 388 optimal weight: 50.0000 overall best weight: 2.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN C 18 HIS ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 ASN F 221 GLN ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN G1027 ASN J 37 ASN Q 93 GLN R 25 ASN R 64 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.124555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085383 restraints weight = 95533.052| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.92 r_work: 0.3214 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 41156 Z= 0.170 Angle : 0.744 9.554 56544 Z= 0.395 Chirality : 0.050 0.274 6419 Planarity : 0.005 0.068 6443 Dihedral : 21.352 174.532 7476 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.10 % Favored : 96.76 % Rotamer: Outliers : 3.17 % Allowed : 12.90 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.12), residues: 4415 helix: -0.17 (0.11), residues: 1982 sheet: -0.38 (0.18), residues: 688 loop : -0.55 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 36 TYR 0.024 0.002 TYR I 178 PHE 0.031 0.002 PHE N 61 TRP 0.024 0.002 TRP G 599 HIS 0.008 0.001 HIS T 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (41156) covalent geometry : angle 0.74450 / 0.39 (56544) hydrogen bonds : bond 0.05186 / 3.44 ( 1696) hydrogen bonds : angle 4.77541 / 3.43 ( 4619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 539 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8627 (m-30) cc_final: 0.8281 (m-30) REVERT: A 400 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8896 (mtpt) REVERT: A 449 ASP cc_start: 0.8727 (m-30) cc_final: 0.8525 (m-30) REVERT: B 15 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8843 (tp) REVERT: C 105 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: C 137 GLU cc_start: 0.8199 (pm20) cc_final: 0.7892 (pm20) REVERT: C 181 GLN cc_start: 0.8608 (pt0) cc_final: 0.8048 (tm-30) REVERT: C 260 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8006 (tpt) REVERT: C 286 TYR cc_start: 0.8097 (m-10) cc_final: 0.7893 (m-10) REVERT: C 359 MET cc_start: 0.8339 (mtp) cc_final: 0.8025 (mtm) REVERT: C 363 THR cc_start: 0.9401 (m) cc_final: 0.9190 (p) REVERT: C 364 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7917 (mmm) REVERT: D 163 LEU cc_start: 0.8798 (mt) cc_final: 0.8481 (mt) REVERT: D 169 GLU cc_start: 0.8496 (tp30) cc_final: 0.8085 (tp30) REVERT: D 313 ASN cc_start: 0.8476 (t0) cc_final: 0.8154 (t0) REVERT: E 46 MET cc_start: 0.7404 (mtp) cc_final: 0.7119 (mtp) REVERT: E 88 MET cc_start: 0.8783 (mmp) cc_final: 0.8303 (mmm) REVERT: E 218 MET cc_start: 0.6574 (tpp) cc_final: 0.6363 (tpp) REVERT: E 303 MET cc_start: 0.8917 (mmp) cc_final: 0.8668 (mmm) REVERT: E 441 GLN cc_start: 0.8379 (tp40) cc_final: 0.8117 (tp40) REVERT: F 34 ASP cc_start: 0.8188 (m-30) cc_final: 0.7955 (p0) REVERT: F 88 MET cc_start: 0.8198 (mmp) cc_final: 0.7886 (mmm) REVERT: F 274 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8587 (tm-30) REVERT: G 593 PHE cc_start: 0.7439 (m-80) cc_final: 0.6848 (m-80) REVERT: G 628 ILE cc_start: 0.7110 (mt) cc_final: 0.6881 (mt) REVERT: G 641 PHE cc_start: 0.7726 (m-80) cc_final: 0.7063 (m-80) REVERT: G 675 ASN cc_start: 0.5940 (OUTLIER) cc_final: 0.5611 (t0) REVERT: G 691 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8134 (mm) REVERT: G 880 LYS cc_start: 0.8432 (mttt) cc_final: 0.8190 (mmtt) REVERT: G 967 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7861 (tt) REVERT: G 1123 TYR cc_start: 0.8325 (m-80) cc_final: 0.7863 (m-80) REVERT: H 272 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7994 (mmm) REVERT: H 273 VAL cc_start: 0.8153 (t) cc_final: 0.7892 (p) REVERT: I 146 GLN cc_start: 0.8254 (mp10) cc_final: 0.7883 (mp10) REVERT: I 206 ILE cc_start: 0.8836 (mt) cc_final: 0.8617 (mt) REVERT: J 93 MET cc_start: 0.3978 (tpt) cc_final: 0.3737 (tpt) REVERT: J 475 ILE cc_start: 0.9420 (pt) cc_final: 0.9157 (mt) REVERT: J 497 ASN cc_start: 0.8702 (m110) cc_final: 0.8356 (m-40) REVERT: M 50 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7935 (mp0) REVERT: M 67 PHE cc_start: 0.8676 (t80) cc_final: 0.8123 (t80) REVERT: M 123 ASP cc_start: 0.7423 (m-30) cc_final: 0.6697 (t0) REVERT: N 44 LYS cc_start: 0.7894 (tptp) cc_final: 0.7549 (tptp) REVERT: N 88 TYR cc_start: 0.7119 (m-10) cc_final: 0.6659 (m-80) REVERT: Q 68 GLN cc_start: 0.7944 (tp40) cc_final: 0.7564 (mm-40) REVERT: Q 134 ARG cc_start: 0.6418 (ttm170) cc_final: 0.5906 (ttm110) REVERT: R 52 GLU cc_start: 0.7882 (pm20) cc_final: 0.7610 (pm20) REVERT: R 63 GLU cc_start: 0.8240 (pt0) cc_final: 0.8034 (pt0) REVERT: R 75 HIS cc_start: 0.7685 (t70) cc_final: 0.7020 (t70) REVERT: R 88 TYR cc_start: 0.7909 (m-80) cc_final: 0.7681 (m-80) REVERT: S 87 ILE cc_start: 0.9006 (mt) cc_final: 0.8713 (mt) REVERT: T 76 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7947 (pt0) REVERT: T 92 ARG cc_start: 0.7294 (ptm160) cc_final: 0.6977 (mtp180) REVERT: T 93 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6317 (mt-10) REVERT: T 113 GLU cc_start: 0.8076 (tp30) cc_final: 0.7723 (tp30) outliers start: 121 outliers final: 76 residues processed: 617 average time/residue: 0.2489 time to fit residues: 251.2763 Evaluate side-chains 570 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 486 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 675 ASN Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 809 VAL Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 958 SER Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1109 LEU Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1185 LEU Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain H residue 272 MET Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 485 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 33 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 5.9990 chunk 425 optimal weight: 6.9990 chunk 400 optimal weight: 50.0000 chunk 299 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 347 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 446 optimal weight: 8.9990 chunk 339 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN F 302 HIS ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 HIS R 25 ASN R 64 ASN ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.121784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080994 restraints weight = 95602.458| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.71 r_work: 0.3159 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 41156 Z= 0.262 Angle : 0.773 15.432 56544 Z= 0.403 Chirality : 0.050 0.269 6419 Planarity : 0.005 0.056 6443 Dihedral : 21.411 174.940 7475 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 3.57 % Allowed : 14.24 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.12), residues: 4415 helix: -0.09 (0.11), residues: 1991 sheet: -0.57 (0.18), residues: 678 loop : -0.65 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 353 TYR 0.026 0.002 TYR R 72 PHE 0.033 0.002 PHE N 61 TRP 0.037 0.002 TRP G 599 HIS 0.012 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.26 (41156) covalent geometry : angle 0.77252 / 0.40 (56544) hydrogen bonds : bond 0.05239 / 3.49 ( 1696) hydrogen bonds : angle 4.78946 / 3.43 ( 4619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 505 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8656 (m-30) cc_final: 0.8227 (m-30) REVERT: C 105 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8433 (mt-10) REVERT: C 137 GLU cc_start: 0.8358 (pm20) cc_final: 0.8037 (pm20) REVERT: C 181 GLN cc_start: 0.8614 (pt0) cc_final: 0.8098 (tm-30) REVERT: C 260 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8151 (tpt) REVERT: C 317 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7450 (tmm-80) REVERT: C 359 MET cc_start: 0.8516 (mtp) cc_final: 0.8246 (mtm) REVERT: C 363 THR cc_start: 0.9423 (m) cc_final: 0.9183 (p) REVERT: C 364 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8079 (mmm) REVERT: D 163 LEU cc_start: 0.8760 (mt) cc_final: 0.8370 (mp) REVERT: D 169 GLU cc_start: 0.8470 (tp30) cc_final: 0.8154 (tp30) REVERT: E 46 MET cc_start: 0.7521 (mtp) cc_final: 0.7233 (mtp) REVERT: E 88 MET cc_start: 0.8855 (mmp) cc_final: 0.8343 (mmm) REVERT: E 218 MET cc_start: 0.6803 (tpp) cc_final: 0.6524 (tpp) REVERT: E 303 MET cc_start: 0.9067 (mmp) cc_final: 0.8747 (mmm) REVERT: F 139 GLU cc_start: 0.8173 (tt0) cc_final: 0.7707 (tp30) REVERT: F 227 CYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8642 (m) REVERT: F 267 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7631 (mm-30) REVERT: G 593 PHE cc_start: 0.7454 (m-80) cc_final: 0.6901 (m-80) REVERT: G 641 PHE cc_start: 0.7903 (m-80) cc_final: 0.7365 (m-80) REVERT: G 684 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7344 (tp) REVERT: G 880 LYS cc_start: 0.8461 (mttt) cc_final: 0.8224 (mmtt) REVERT: G 967 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8058 (tt) REVERT: G 1123 TYR cc_start: 0.8476 (m-80) cc_final: 0.8058 (m-80) REVERT: H 272 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: I 146 GLN cc_start: 0.8321 (mp10) cc_final: 0.7869 (mp10) REVERT: I 206 ILE cc_start: 0.8804 (mt) cc_final: 0.8559 (mp) REVERT: J 93 MET cc_start: 0.4238 (tpt) cc_final: 0.4004 (tpp) REVERT: J 276 MET cc_start: 0.1836 (mmp) cc_final: 0.1195 (mmp) REVERT: J 475 ILE cc_start: 0.9445 (pt) cc_final: 0.9129 (mt) REVERT: J 497 ASN cc_start: 0.8749 (m110) cc_final: 0.8452 (m-40) REVERT: M 50 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7927 (mp0) REVERT: M 67 PHE cc_start: 0.8721 (t80) cc_final: 0.8356 (t80) REVERT: M 107 THR cc_start: 0.8535 (m) cc_final: 0.8088 (t) REVERT: M 123 ASP cc_start: 0.7412 (m-30) cc_final: 0.6818 (t0) REVERT: N 44 LYS cc_start: 0.8042 (tptp) cc_final: 0.7742 (tptp) REVERT: Q 68 GLN cc_start: 0.7835 (tp40) cc_final: 0.7542 (mm-40) REVERT: Q 97 GLU cc_start: 0.8924 (tt0) cc_final: 0.8245 (tp30) REVERT: Q 115 LYS cc_start: 0.7678 (tptt) cc_final: 0.7373 (tttt) REVERT: Q 134 ARG cc_start: 0.6487 (ttm170) cc_final: 0.6060 (ttm-80) REVERT: R 52 GLU cc_start: 0.7953 (pm20) cc_final: 0.7669 (pm20) REVERT: R 72 TYR cc_start: 0.8068 (m-80) cc_final: 0.7707 (m-80) REVERT: R 75 HIS cc_start: 0.7619 (t70) cc_final: 0.7161 (t70) REVERT: R 88 TYR cc_start: 0.7923 (m-80) cc_final: 0.7625 (m-80) REVERT: T 76 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7829 (pt0) REVERT: T 92 ARG cc_start: 0.7173 (ptm160) cc_final: 0.6851 (mtp180) REVERT: T 93 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6372 (mt-10) REVERT: T 113 GLU cc_start: 0.8086 (tp30) cc_final: 0.7672 (tp30) outliers start: 136 outliers final: 94 residues processed: 596 average time/residue: 0.2551 time to fit residues: 250.1848 Evaluate side-chains 567 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 466 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 227 CYS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 809 VAL Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 882 ILE Chi-restraints excluded: chain G residue 958 SER Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain G residue 1249 ILE Chi-restraints excluded: chain H residue 272 MET Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 527 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 87 optimal weight: 9.9990 chunk 335 optimal weight: 0.0040 chunk 104 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 391 optimal weight: 50.0000 chunk 128 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN B 348 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 675 ASN R 25 ASN R 64 ASN S 73 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.123536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084059 restraints weight = 94645.960| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.88 r_work: 0.3188 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41156 Z= 0.159 Angle : 0.688 12.139 56544 Z= 0.361 Chirality : 0.047 0.266 6419 Planarity : 0.004 0.067 6443 Dihedral : 21.324 174.733 7475 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.28 % Favored : 96.58 % Rotamer: Outliers : 3.38 % Allowed : 15.39 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 4415 helix: 0.19 (0.12), residues: 1986 sheet: -0.42 (0.19), residues: 681 loop : -0.62 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 208 TYR 0.025 0.001 TYR N 72 PHE 0.026 0.001 PHE T 65 TRP 0.045 0.002 TRP G 599 HIS 0.014 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (41156) covalent geometry : angle 0.68750 / 0.36 (56544) hydrogen bonds : bond 0.04563 / 3.03 ( 1696) hydrogen bonds : angle 4.51618 / 3.25 ( 4619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 512 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8600 (m-30) cc_final: 0.8137 (m-30) REVERT: A 449 ASP cc_start: 0.8689 (m-30) cc_final: 0.8470 (m-30) REVERT: B 54 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: B 405 TYR cc_start: 0.8778 (t80) cc_final: 0.8535 (t80) REVERT: C 105 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: C 137 GLU cc_start: 0.8323 (pm20) cc_final: 0.8007 (pm20) REVERT: C 181 GLN cc_start: 0.8571 (pt0) cc_final: 0.7994 (tm-30) REVERT: C 260 MET cc_start: 0.8508 (ttm) cc_final: 0.8066 (tpt) REVERT: C 317 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7436 (tmm-80) REVERT: C 359 MET cc_start: 0.8617 (mtp) cc_final: 0.8376 (mtm) REVERT: C 363 THR cc_start: 0.9419 (m) cc_final: 0.9200 (p) REVERT: D 147 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8271 (pt) REVERT: D 163 LEU cc_start: 0.8711 (mt) cc_final: 0.8488 (mp) REVERT: D 169 GLU cc_start: 0.8489 (tp30) cc_final: 0.8156 (tp30) REVERT: D 303 MET cc_start: 0.8890 (mmm) cc_final: 0.8345 (mmm) REVERT: E 46 MET cc_start: 0.7450 (mtp) cc_final: 0.7219 (mtp) REVERT: E 88 MET cc_start: 0.8777 (mmp) cc_final: 0.8284 (mmm) REVERT: E 303 MET cc_start: 0.9010 (mmp) cc_final: 0.8735 (mmm) REVERT: E 441 GLN cc_start: 0.8384 (tp40) cc_final: 0.8137 (tp40) REVERT: F 88 MET cc_start: 0.8219 (mmp) cc_final: 0.7883 (mmm) REVERT: F 139 GLU cc_start: 0.8119 (tt0) cc_final: 0.7664 (tp30) REVERT: F 185 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8474 (t70) REVERT: G 593 PHE cc_start: 0.7420 (m-80) cc_final: 0.6925 (m-80) REVERT: G 641 PHE cc_start: 0.8191 (m-80) cc_final: 0.7493 (m-80) REVERT: G 691 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8199 (mm) REVERT: G 810 MET cc_start: 0.7370 (mmt) cc_final: 0.7109 (mmt) REVERT: G 880 LYS cc_start: 0.8532 (mttt) cc_final: 0.8233 (mmtt) REVERT: G 967 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8022 (tt) REVERT: G 1123 TYR cc_start: 0.8438 (m-80) cc_final: 0.8001 (m-80) REVERT: G 1236 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8044 (tp-100) REVERT: H 272 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: I 120 LYS cc_start: 0.7880 (mttm) cc_final: 0.7387 (tttm) REVERT: I 151 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7518 (mt-10) REVERT: I 206 ILE cc_start: 0.8823 (mt) cc_final: 0.8507 (mp) REVERT: J 213 LEU cc_start: 0.9000 (mp) cc_final: 0.8718 (mp) REVERT: J 263 TRP cc_start: 0.8810 (m100) cc_final: 0.8528 (m100) REVERT: J 276 MET cc_start: 0.1785 (mmp) cc_final: 0.1382 (mmp) REVERT: J 475 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9135 (mt) REVERT: J 497 ASN cc_start: 0.8772 (m110) cc_final: 0.8433 (m-40) REVERT: M 50 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7941 (mp0) REVERT: M 67 PHE cc_start: 0.8741 (t80) cc_final: 0.8319 (t80) REVERT: M 93 GLN cc_start: 0.7243 (tt0) cc_final: 0.6984 (mt0) REVERT: M 107 THR cc_start: 0.8588 (m) cc_final: 0.8268 (p) REVERT: M 123 ASP cc_start: 0.7317 (m-30) cc_final: 0.6649 (t0) REVERT: N 44 LYS cc_start: 0.8078 (tptp) cc_final: 0.7847 (tmtt) REVERT: N 84 MET cc_start: 0.7437 (mpp) cc_final: 0.6946 (mpp) REVERT: N 88 TYR cc_start: 0.7579 (m-10) cc_final: 0.7240 (m-80) REVERT: Q 68 GLN cc_start: 0.7716 (tp40) cc_final: 0.7469 (mm-40) REVERT: Q 97 GLU cc_start: 0.8947 (tt0) cc_final: 0.8250 (tp30) REVERT: Q 105 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8130 (tp30) REVERT: Q 115 LYS cc_start: 0.7684 (tptt) cc_final: 0.7407 (tttt) REVERT: Q 134 ARG cc_start: 0.6500 (ttm170) cc_final: 0.6042 (ttm-80) REVERT: R 52 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: R 63 GLU cc_start: 0.7985 (pt0) cc_final: 0.7686 (pm20) REVERT: R 75 HIS cc_start: 0.7667 (t70) cc_final: 0.7222 (t70) REVERT: R 88 TYR cc_start: 0.7959 (m-80) cc_final: 0.7585 (m-80) REVERT: T 76 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7729 (pt0) REVERT: T 92 ARG cc_start: 0.7231 (ptm160) cc_final: 0.6683 (mmm160) REVERT: T 93 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6573 (mt-10) REVERT: T 113 GLU cc_start: 0.8079 (tp30) cc_final: 0.7555 (tp30) outliers start: 129 outliers final: 85 residues processed: 604 average time/residue: 0.2390 time to fit residues: 238.0297 Evaluate side-chains 571 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 475 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 809 VAL Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 958 SER Chi-restraints excluded: chain G residue 967 LEU Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1181 LEU Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain G residue 1249 ILE Chi-restraints excluded: chain H residue 272 MET Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 204 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 485 GLU Chi-restraints excluded: chain M residue 78 PHE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 447 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 370 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 413 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS E 221 GLN ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 ASN J 207 ASN R 25 ASN R 64 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.122621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083333 restraints weight = 95767.019| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.89 r_work: 0.3171 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41156 Z= 0.193 Angle : 0.698 13.417 56544 Z= 0.363 Chirality : 0.047 0.265 6419 Planarity : 0.004 0.046 6443 Dihedral : 21.321 175.182 7475 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 3.70 % Allowed : 16.15 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 4415 helix: 0.22 (0.12), residues: 1994 sheet: -0.46 (0.19), residues: 680 loop : -0.68 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 208 TYR 0.037 0.002 TYR R 72 PHE 0.031 0.001 PHE M 78 TRP 0.027 0.002 TRP G 646 HIS 0.008 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (41156) covalent geometry : angle 0.69823 / 0.36 (56544) hydrogen bonds : bond 0.04610 / 3.06 ( 1696) hydrogen bonds : angle 4.52256 / 3.25 ( 4619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 484 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.8637 (m-30) cc_final: 0.8179 (m-30) REVERT: A 449 ASP cc_start: 0.8705 (m-30) cc_final: 0.8478 (m-30) REVERT: B 54 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: C 105 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: C 137 GLU cc_start: 0.8385 (pm20) cc_final: 0.8035 (pm20) REVERT: C 181 GLN cc_start: 0.8542 (pt0) cc_final: 0.8035 (tm-30) REVERT: C 260 MET cc_start: 0.8562 (ttm) cc_final: 0.8188 (tpt) REVERT: C 317 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7378 (tmm-80) REVERT: C 363 THR cc_start: 0.9438 (m) cc_final: 0.9208 (p) REVERT: C 364 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8108 (mmm) REVERT: D 147 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8306 (pt) REVERT: D 163 LEU cc_start: 0.8657 (mt) cc_final: 0.8225 (mp) REVERT: D 169 GLU cc_start: 0.8470 (tp30) cc_final: 0.8047 (tp30) REVERT: E 46 MET cc_start: 0.7516 (mtp) cc_final: 0.7206 (mtp) REVERT: E 88 MET cc_start: 0.8852 (mmp) cc_final: 0.8272 (mmm) REVERT: E 218 MET cc_start: 0.6576 (tpp) cc_final: 0.6338 (tpp) REVERT: E 303 MET cc_start: 0.9028 (mmp) cc_final: 0.8759 (mmm) REVERT: F 185 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8500 (t70) REVERT: G 593 PHE cc_start: 0.7374 (m-80) cc_final: 0.6733 (m-80) REVERT: G 641 PHE cc_start: 0.8109 (m-80) cc_final: 0.7490 (m-80) REVERT: G 684 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7349 (tp) REVERT: G 810 MET cc_start: 0.7385 (mmt) cc_final: 0.7130 (mmt) REVERT: G 880 LYS cc_start: 0.8567 (mttt) cc_final: 0.8238 (mmtt) REVERT: G 1123 TYR cc_start: 0.8408 (m-80) cc_final: 0.7946 (m-80) REVERT: G 1236 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: H 272 MET cc_start: 0.8868 (mmt) cc_final: 0.8126 (mmm) REVERT: I 120 LYS cc_start: 0.7931 (mttm) cc_final: 0.7388 (tttm) REVERT: I 206 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8566 (mp) REVERT: J 93 MET cc_start: 0.3994 (tpt) cc_final: 0.3744 (tpp) REVERT: J 263 TRP cc_start: 0.8788 (m100) cc_final: 0.8535 (m100) REVERT: J 276 MET cc_start: 0.1686 (mmp) cc_final: 0.1261 (mmp) REVERT: J 475 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9149 (mt) REVERT: J 497 ASN cc_start: 0.8781 (m110) cc_final: 0.8464 (m-40) REVERT: M 50 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7973 (mp0) REVERT: M 67 PHE cc_start: 0.8689 (t80) cc_final: 0.8370 (t80) REVERT: M 93 GLN cc_start: 0.7279 (tt0) cc_final: 0.7021 (mt0) REVERT: M 107 THR cc_start: 0.8617 (m) cc_final: 0.8281 (p) REVERT: M 123 ASP cc_start: 0.7282 (m-30) cc_final: 0.6596 (t0) REVERT: Q 68 GLN cc_start: 0.7696 (tp40) cc_final: 0.7456 (mm-40) REVERT: Q 97 GLU cc_start: 0.8960 (tt0) cc_final: 0.8253 (tp30) REVERT: Q 105 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8138 (tp30) REVERT: Q 115 LYS cc_start: 0.7664 (tptt) cc_final: 0.7344 (tttt) REVERT: Q 134 ARG cc_start: 0.6520 (ttm170) cc_final: 0.6058 (ttm-80) REVERT: R 52 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: R 63 GLU cc_start: 0.8021 (pt0) cc_final: 0.7774 (pt0) REVERT: R 75 HIS cc_start: 0.7623 (t70) cc_final: 0.7234 (t70) REVERT: R 88 TYR cc_start: 0.7886 (m-80) cc_final: 0.7666 (m-80) REVERT: T 76 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7580 (pt0) REVERT: T 113 GLU cc_start: 0.8056 (tp30) cc_final: 0.7624 (tp30) outliers start: 141 outliers final: 98 residues processed: 584 average time/residue: 0.2316 time to fit residues: 223.8694 Evaluate side-chains 574 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 465 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1181 LEU Chi-restraints excluded: chain G residue 1220 THR Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain G residue 1249 ILE Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 173 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 393 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 419 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 304 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 343 optimal weight: 8.9990 chunk 256 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS B 181 GLN ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 64 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.126225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088355 restraints weight = 92938.408| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.48 r_work: 0.3282 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41156 Z= 0.141 Angle : 0.672 15.119 56544 Z= 0.349 Chirality : 0.046 0.246 6419 Planarity : 0.004 0.043 6443 Dihedral : 21.301 176.460 7475 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 3.54 % Allowed : 16.96 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.13), residues: 4415 helix: 0.38 (0.12), residues: 1988 sheet: -0.38 (0.19), residues: 672 loop : -0.62 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 208 TYR 0.031 0.001 TYR N 72 PHE 0.028 0.001 PHE T 65 TRP 0.020 0.002 TRP G 599 HIS 0.013 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (41156) covalent geometry : angle 0.67211 / 0.35 (56544) hydrogen bonds : bond 0.04292 / 2.85 ( 1696) hydrogen bonds : angle 4.36552 / 3.15 ( 4619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 503 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8338 (mptt) REVERT: B 54 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: C 137 GLU cc_start: 0.8368 (pm20) cc_final: 0.8140 (pm20) REVERT: C 181 GLN cc_start: 0.8420 (pt0) cc_final: 0.8089 (tm-30) REVERT: C 260 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8210 (tpt) REVERT: C 317 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7457 (tmm-80) REVERT: C 363 THR cc_start: 0.9388 (m) cc_final: 0.9170 (p) REVERT: C 364 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: D 147 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8205 (pt) REVERT: D 163 LEU cc_start: 0.8776 (mt) cc_final: 0.8540 (mm) REVERT: D 169 GLU cc_start: 0.8414 (tp30) cc_final: 0.8174 (tp30) REVERT: D 303 MET cc_start: 0.8802 (mmm) cc_final: 0.8303 (mmm) REVERT: E 88 MET cc_start: 0.8664 (mmp) cc_final: 0.8311 (mmm) REVERT: E 191 ASP cc_start: 0.7658 (m-30) cc_final: 0.7001 (m-30) REVERT: F 88 MET cc_start: 0.8289 (mmp) cc_final: 0.8025 (mmm) REVERT: G 593 PHE cc_start: 0.7457 (m-80) cc_final: 0.7037 (m-80) REVERT: G 641 PHE cc_start: 0.8185 (m-80) cc_final: 0.7643 (m-80) REVERT: G 691 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8285 (mm) REVERT: G 810 MET cc_start: 0.7623 (mmt) cc_final: 0.7333 (mmt) REVERT: G 880 LYS cc_start: 0.8474 (mttt) cc_final: 0.8218 (mmtt) REVERT: G 1123 TYR cc_start: 0.8616 (m-80) cc_final: 0.8105 (m-80) REVERT: G 1236 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: H 272 MET cc_start: 0.8928 (mmt) cc_final: 0.8269 (mmm) REVERT: I 139 ARG cc_start: 0.3925 (mtt180) cc_final: 0.3201 (tpm170) REVERT: I 146 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8236 (mm-40) REVERT: I 206 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8685 (mp) REVERT: J 65 CYS cc_start: 0.4711 (OUTLIER) cc_final: 0.4005 (m) REVERT: J 93 MET cc_start: 0.4962 (tpt) cc_final: 0.4602 (tpp) REVERT: J 276 MET cc_start: 0.2314 (mmp) cc_final: 0.2039 (mmp) REVERT: J 464 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8345 (pp20) REVERT: J 475 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9133 (mt) REVERT: J 481 LYS cc_start: 0.8721 (pptt) cc_final: 0.8224 (tptp) REVERT: M 50 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7933 (mp0) REVERT: M 67 PHE cc_start: 0.8692 (t80) cc_final: 0.8357 (t80) REVERT: M 93 GLN cc_start: 0.7453 (tt0) cc_final: 0.7183 (mt0) REVERT: M 107 THR cc_start: 0.8723 (m) cc_final: 0.8414 (p) REVERT: M 123 ASP cc_start: 0.7180 (m-30) cc_final: 0.6667 (t0) REVERT: N 39 ARG cc_start: 0.8663 (tpp-160) cc_final: 0.8432 (tpp-160) REVERT: N 44 LYS cc_start: 0.7558 (tptp) cc_final: 0.7045 (tptt) REVERT: Q 97 GLU cc_start: 0.8945 (tt0) cc_final: 0.8181 (tp30) REVERT: Q 105 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8219 (tp30) REVERT: Q 115 LYS cc_start: 0.7778 (tptt) cc_final: 0.7455 (tttt) REVERT: Q 134 ARG cc_start: 0.6480 (ttm170) cc_final: 0.6030 (ttm-80) REVERT: R 52 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: R 63 GLU cc_start: 0.8124 (pt0) cc_final: 0.7859 (pt0) REVERT: R 88 TYR cc_start: 0.7889 (m-80) cc_final: 0.7653 (m-80) REVERT: T 76 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7513 (pt0) REVERT: T 113 GLU cc_start: 0.7969 (tp30) cc_final: 0.7505 (tp30) outliers start: 135 outliers final: 92 residues processed: 597 average time/residue: 0.2276 time to fit residues: 223.2682 Evaluate side-chains 572 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 468 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1088 ILE Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1181 LEU Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain G residue 1249 ILE Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 485 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 349 optimal weight: 10.0000 chunk 439 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 411 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 878 HIS ** J 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 64 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 84 ASN T 95 GLN T 109 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.121971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081419 restraints weight = 95334.442| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.95 r_work: 0.3149 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 41156 Z= 0.227 Angle : 0.717 14.689 56544 Z= 0.369 Chirality : 0.047 0.253 6419 Planarity : 0.004 0.042 6443 Dihedral : 21.356 177.087 7475 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.29 % Rotamer: Outliers : 3.72 % Allowed : 17.15 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4415 helix: 0.35 (0.12), residues: 1988 sheet: -0.50 (0.19), residues: 685 loop : -0.70 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 336 TYR 0.033 0.002 TYR B 405 PHE 0.028 0.002 PHE T 65 TRP 0.016 0.002 TRP G 612 HIS 0.015 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (41156) covalent geometry : angle 0.71721 / 0.37 (56544) hydrogen bonds : bond 0.04648 / 3.07 ( 1696) hydrogen bonds : angle 4.51708 / 3.25 ( 4619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 471 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8306 (mptt) REVERT: A 244 ASP cc_start: 0.8608 (m-30) cc_final: 0.8059 (m-30) REVERT: B 54 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: C 137 GLU cc_start: 0.8436 (pm20) cc_final: 0.8093 (pm20) REVERT: C 181 GLN cc_start: 0.8509 (pt0) cc_final: 0.8141 (tm-30) REVERT: C 260 MET cc_start: 0.8573 (ttm) cc_final: 0.8261 (tpt) REVERT: C 317 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7402 (tmm-80) REVERT: C 359 MET cc_start: 0.8597 (mtp) cc_final: 0.8377 (mtm) REVERT: C 364 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: D 147 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8311 (pt) REVERT: D 169 GLU cc_start: 0.8387 (tp30) cc_final: 0.8045 (tp30) REVERT: D 303 MET cc_start: 0.8940 (mmm) cc_final: 0.8378 (mmm) REVERT: E 88 MET cc_start: 0.8828 (mmp) cc_final: 0.8307 (mmm) REVERT: E 191 ASP cc_start: 0.7501 (m-30) cc_final: 0.6677 (m-30) REVERT: F 88 MET cc_start: 0.8302 (mmp) cc_final: 0.7965 (mmm) REVERT: F 185 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8200 (t70) REVERT: G 593 PHE cc_start: 0.7424 (m-80) cc_final: 0.6805 (m-80) REVERT: G 641 PHE cc_start: 0.8250 (m-80) cc_final: 0.7671 (m-80) REVERT: G 684 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7261 (tp) REVERT: G 810 MET cc_start: 0.7536 (mmt) cc_final: 0.7278 (mmt) REVERT: G 880 LYS cc_start: 0.8593 (mttt) cc_final: 0.8247 (mmtt) REVERT: G 1123 TYR cc_start: 0.8497 (m-80) cc_final: 0.7978 (m-80) REVERT: G 1236 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8550 (pt0) REVERT: H 272 MET cc_start: 0.8900 (mmt) cc_final: 0.8185 (mmm) REVERT: I 139 ARG cc_start: 0.3992 (mtt180) cc_final: 0.3281 (tpm170) REVERT: I 206 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8737 (mp) REVERT: J 65 CYS cc_start: 0.5027 (OUTLIER) cc_final: 0.4316 (m) REVERT: J 93 MET cc_start: 0.4281 (tpt) cc_final: 0.4033 (tpp) REVERT: J 101 ASN cc_start: 0.7914 (p0) cc_final: 0.6702 (p0) REVERT: J 276 MET cc_start: 0.1977 (mmp) cc_final: 0.1567 (mmp) REVERT: J 464 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8282 (pp20) REVERT: J 475 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9162 (mt) REVERT: J 481 LYS cc_start: 0.8655 (pptt) cc_final: 0.8139 (tptp) REVERT: J 497 ASN cc_start: 0.8786 (m110) cc_final: 0.8466 (m-40) REVERT: M 50 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7894 (mp0) REVERT: M 67 PHE cc_start: 0.8630 (t80) cc_final: 0.8350 (t80) REVERT: M 93 GLN cc_start: 0.7430 (tt0) cc_final: 0.7135 (tt0) REVERT: M 107 THR cc_start: 0.8693 (m) cc_final: 0.8234 (p) REVERT: M 123 ASP cc_start: 0.7187 (m-30) cc_final: 0.6577 (t70) REVERT: N 39 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8285 (tpp-160) REVERT: Q 97 GLU cc_start: 0.8969 (tt0) cc_final: 0.8204 (tp30) REVERT: Q 105 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8220 (tp30) REVERT: Q 115 LYS cc_start: 0.7789 (tptt) cc_final: 0.7470 (tttt) REVERT: Q 134 ARG cc_start: 0.6515 (ttm170) cc_final: 0.6060 (ttm-80) REVERT: R 52 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: T 76 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7531 (pt0) REVERT: T 113 GLU cc_start: 0.8051 (tp30) cc_final: 0.7580 (tp30) outliers start: 142 outliers final: 104 residues processed: 567 average time/residue: 0.2507 time to fit residues: 234.2300 Evaluate side-chains 574 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 458 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 677 LEU Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1181 LEU Chi-restraints excluded: chain G residue 1185 LEU Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain G residue 1249 ILE Chi-restraints excluded: chain H residue 283 THR Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 514 MET Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 421 optimal weight: 30.0000 chunk 427 optimal weight: 20.0000 chunk 213 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 372 optimal weight: 7.9990 chunk 395 optimal weight: 50.0000 chunk 254 optimal weight: 5.9990 chunk 435 optimal weight: 5.9990 chunk 448 optimal weight: 30.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 64 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 GLN T 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.125032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.086469 restraints weight = 94676.774| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.56 r_work: 0.3245 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41156 Z= 0.182 Angle : 0.691 15.484 56544 Z= 0.357 Chirality : 0.046 0.252 6419 Planarity : 0.004 0.058 6443 Dihedral : 21.368 177.766 7475 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.42 % Favored : 96.44 % Rotamer: Outliers : 3.51 % Allowed : 17.83 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.13), residues: 4415 helix: 0.37 (0.12), residues: 1982 sheet: -0.51 (0.19), residues: 674 loop : -0.71 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 208 TYR 0.029 0.002 TYR N 72 PHE 0.027 0.001 PHE T 65 TRP 0.022 0.002 TRP G 582 HIS 0.007 0.001 HIS J 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (41156) covalent geometry : angle 0.69095 / 0.36 (56544) hydrogen bonds : bond 0.04406 / 2.91 ( 1696) hydrogen bonds : angle 4.47040 / 3.22 ( 4619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 476 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8396 (mptt) REVERT: B 54 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 137 GLU cc_start: 0.8451 (pm20) cc_final: 0.8169 (pm20) REVERT: C 181 GLN cc_start: 0.8427 (pt0) cc_final: 0.8160 (tm-30) REVERT: C 260 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8326 (tpt) REVERT: C 286 TYR cc_start: 0.8074 (m-10) cc_final: 0.7873 (m-10) REVERT: C 317 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7493 (tmm-80) REVERT: C 418 LYS cc_start: 0.8882 (mptt) cc_final: 0.8681 (mptt) REVERT: D 147 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8277 (pt) REVERT: D 163 LEU cc_start: 0.8791 (mt) cc_final: 0.8505 (mm) REVERT: D 169 GLU cc_start: 0.8439 (tp30) cc_final: 0.8178 (tp30) REVERT: E 46 MET cc_start: 0.8044 (mtp) cc_final: 0.7818 (ptp) REVERT: E 88 MET cc_start: 0.8776 (mmp) cc_final: 0.8362 (mmm) REVERT: E 191 ASP cc_start: 0.7727 (m-30) cc_final: 0.6979 (m-30) REVERT: F 88 MET cc_start: 0.8421 (mmp) cc_final: 0.8067 (mmm) REVERT: F 185 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8212 (t70) REVERT: G 593 PHE cc_start: 0.7465 (m-80) cc_final: 0.6935 (m-80) REVERT: G 641 PHE cc_start: 0.8265 (m-80) cc_final: 0.7685 (m-80) REVERT: G 684 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7205 (tp) REVERT: G 810 MET cc_start: 0.7661 (mmt) cc_final: 0.7387 (mmt) REVERT: G 880 LYS cc_start: 0.8547 (mttt) cc_final: 0.8236 (mmtt) REVERT: G 1123 TYR cc_start: 0.8625 (m-80) cc_final: 0.8080 (m-80) REVERT: G 1236 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8553 (pt0) REVERT: I 139 ARG cc_start: 0.3985 (mtt180) cc_final: 0.3368 (tpm170) REVERT: I 206 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8752 (mp) REVERT: J 65 CYS cc_start: 0.4811 (OUTLIER) cc_final: 0.4185 (m) REVERT: J 93 MET cc_start: 0.4926 (tpt) cc_final: 0.4598 (tpp) REVERT: J 263 TRP cc_start: 0.8835 (m100) cc_final: 0.8179 (m100) REVERT: J 276 MET cc_start: 0.2365 (mmp) cc_final: 0.2026 (mmp) REVERT: J 464 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8380 (pp20) REVERT: J 475 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9161 (mt) REVERT: J 481 LYS cc_start: 0.8696 (pptt) cc_final: 0.8207 (tptp) REVERT: M 50 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7897 (mp0) REVERT: M 67 PHE cc_start: 0.8656 (t80) cc_final: 0.8416 (t80) REVERT: M 93 GLN cc_start: 0.7496 (tt0) cc_final: 0.7172 (tt0) REVERT: M 107 THR cc_start: 0.8724 (m) cc_final: 0.8275 (p) REVERT: M 123 ASP cc_start: 0.7114 (m-30) cc_final: 0.6643 (t70) REVERT: N 39 ARG cc_start: 0.8584 (tpp-160) cc_final: 0.8332 (tpp-160) REVERT: N 88 TYR cc_start: 0.7625 (m-10) cc_final: 0.7409 (m-80) REVERT: Q 97 GLU cc_start: 0.8958 (tt0) cc_final: 0.8192 (tp30) REVERT: Q 105 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8247 (tp30) REVERT: Q 115 LYS cc_start: 0.7851 (tptt) cc_final: 0.7496 (tttt) REVERT: Q 134 ARG cc_start: 0.6508 (ttm170) cc_final: 0.6056 (ttm-80) REVERT: R 52 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: R 63 GLU cc_start: 0.7959 (pt0) cc_final: 0.7725 (pm20) REVERT: T 76 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7526 (pt0) REVERT: T 113 GLU cc_start: 0.7961 (tp30) cc_final: 0.7501 (tp30) outliers start: 134 outliers final: 105 residues processed: 569 average time/residue: 0.2460 time to fit residues: 230.8979 Evaluate side-chains 573 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 456 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 675 ASN Chi-restraints excluded: chain G residue 684 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1028 ASP Chi-restraints excluded: chain G residue 1120 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1185 LEU Chi-restraints excluded: chain G residue 1221 VAL Chi-restraints excluded: chain G residue 1236 GLN Chi-restraints excluded: chain G residue 1249 ILE Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 514 MET Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 38 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 315 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 234 optimal weight: 6.9990 chunk 450 optimal weight: 8.9990 chunk 331 optimal weight: 0.0020 chunk 382 optimal weight: 7.9990 chunk 344 optimal weight: 0.0670 chunk 268 optimal weight: 8.9990 chunk 279 optimal weight: 0.0570 chunk 314 optimal weight: 6.9990 overall best weight: 0.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 GLN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 64 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.130567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092003 restraints weight = 93230.773| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.73 r_work: 0.3285 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41156 Z= 0.127 Angle : 0.690 18.216 56544 Z= 0.352 Chirality : 0.045 0.253 6419 Planarity : 0.004 0.066 6443 Dihedral : 21.293 177.669 7475 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.13 % Favored : 96.74 % Rotamer: Outliers : 2.28 % Allowed : 19.40 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4415 helix: 0.50 (0.12), residues: 1985 sheet: -0.41 (0.19), residues: 670 loop : -0.62 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 223 TYR 0.031 0.001 TYR N 72 PHE 0.028 0.001 PHE T 65 TRP 0.018 0.002 TRP J 540 HIS 0.005 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (41156) covalent geometry : angle 0.69025 / 0.35 (56544) hydrogen bonds : bond 0.04064 / 2.68 ( 1696) hydrogen bonds : angle 4.29052 / 3.09 ( 4619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 520 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8312 (mptt) REVERT: B 54 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: C 137 GLU cc_start: 0.8265 (pm20) cc_final: 0.8033 (pm20) REVERT: C 165 LYS cc_start: 0.9046 (tttp) cc_final: 0.8788 (mptt) REVERT: C 260 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8137 (tpt) REVERT: C 317 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7445 (tmm-80) REVERT: C 418 LYS cc_start: 0.8799 (mptt) cc_final: 0.8591 (mptt) REVERT: D 147 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8178 (pt) REVERT: D 169 GLU cc_start: 0.8240 (tp30) cc_final: 0.8039 (tp30) REVERT: D 178 MET cc_start: 0.8976 (tpp) cc_final: 0.8602 (tpp) REVERT: D 303 MET cc_start: 0.8677 (mmm) cc_final: 0.8447 (mmm) REVERT: E 88 MET cc_start: 0.8557 (mmp) cc_final: 0.8242 (mmm) REVERT: E 174 LEU cc_start: 0.8996 (mt) cc_final: 0.8784 (mt) REVERT: E 191 ASP cc_start: 0.7463 (m-30) cc_final: 0.6721 (m-30) REVERT: F 88 MET cc_start: 0.8169 (mmp) cc_final: 0.7859 (mmm) REVERT: F 162 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7708 (p) REVERT: F 300 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8224 (mm-30) REVERT: G 593 PHE cc_start: 0.7460 (m-80) cc_final: 0.6954 (m-80) REVERT: G 641 PHE cc_start: 0.8251 (m-80) cc_final: 0.7660 (m-80) REVERT: G 691 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8172 (mt) REVERT: G 810 MET cc_start: 0.7470 (mmt) cc_final: 0.7263 (mmt) REVERT: G 880 LYS cc_start: 0.8461 (mttt) cc_final: 0.8207 (mmtt) REVERT: G 901 MET cc_start: 0.8772 (tpp) cc_final: 0.8439 (tpp) REVERT: G 1027 ASN cc_start: 0.8271 (t0) cc_final: 0.7618 (t0) REVERT: G 1123 TYR cc_start: 0.8504 (m-80) cc_final: 0.7967 (m-80) REVERT: I 139 ARG cc_start: 0.3970 (mtt180) cc_final: 0.3450 (tpm170) REVERT: I 206 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8739 (mp) REVERT: J 65 CYS cc_start: 0.4362 (OUTLIER) cc_final: 0.3876 (m) REVERT: J 93 MET cc_start: 0.4635 (tpt) cc_final: 0.4372 (tpp) REVERT: J 142 LEU cc_start: 0.8925 (mt) cc_final: 0.8379 (pt) REVERT: J 263 TRP cc_start: 0.8756 (m100) cc_final: 0.8126 (m100) REVERT: J 464 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8195 (pp20) REVERT: J 481 LYS cc_start: 0.8666 (pptt) cc_final: 0.8188 (tptt) REVERT: M 51 ILE cc_start: 0.7739 (mm) cc_final: 0.7023 (mt) REVERT: M 67 PHE cc_start: 0.8631 (t80) cc_final: 0.8358 (t80) REVERT: M 93 GLN cc_start: 0.7396 (tt0) cc_final: 0.7097 (tt0) REVERT: M 107 THR cc_start: 0.8701 (m) cc_final: 0.8255 (p) REVERT: M 123 ASP cc_start: 0.7012 (m-30) cc_final: 0.6568 (t70) REVERT: N 39 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8270 (tpp-160) REVERT: N 88 TYR cc_start: 0.7301 (m-10) cc_final: 0.6935 (m-80) REVERT: Q 97 GLU cc_start: 0.8945 (tt0) cc_final: 0.8193 (tp30) REVERT: Q 105 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8198 (tp30) REVERT: Q 106 ASP cc_start: 0.8504 (m-30) cc_final: 0.8212 (m-30) REVERT: Q 134 ARG cc_start: 0.6441 (ttm170) cc_final: 0.5994 (ttm-80) REVERT: R 52 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: S 25 PHE cc_start: 0.7323 (m-80) cc_final: 0.6946 (m-80) REVERT: T 76 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7478 (pt0) REVERT: T 113 GLU cc_start: 0.7841 (tp30) cc_final: 0.7486 (tp30) outliers start: 87 outliers final: 68 residues processed: 581 average time/residue: 0.2376 time to fit residues: 225.5676 Evaluate side-chains 555 residues out of total 3814 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 477 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain G residue 691 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 816 CYS Chi-restraints excluded: chain G residue 980 VAL Chi-restraints excluded: chain G residue 1148 ASP Chi-restraints excluded: chain G residue 1185 LEU Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 129 HIS Chi-restraints excluded: chain I residue 164 PHE Chi-restraints excluded: chain I residue 206 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 65 CYS Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 31 HIS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain T residue 33 ARG Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 65 PHE Chi-restraints excluded: chain T residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 436 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 340 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 325 optimal weight: 6.9990 chunk 334 optimal weight: 0.0170 chunk 11 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 429 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 304 optimal weight: 0.0670 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.124695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084464 restraints weight = 95318.166| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.73 r_work: 0.3196 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41156 Z= 0.134 Angle : 0.676 15.688 56544 Z= 0.347 Chirality : 0.045 0.277 6419 Planarity : 0.004 0.058 6443 Dihedral : 21.289 177.887 7474 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 2.46 % Allowed : 19.32 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4415 helix: 0.53 (0.12), residues: 1993 sheet: -0.38 (0.19), residues: 676 loop : -0.61 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 208 TYR 0.039 0.001 TYR N 72 PHE 0.028 0.001 PHE T 65 TRP 0.028 0.002 TRP G 582 HIS 0.009 0.001 HIS G 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (41156) covalent geometry : angle 0.67617 / 0.35 (56544) hydrogen bonds : bond 0.04066 / 2.67 ( 1696) hydrogen bonds : angle 4.31457 / 3.11 ( 4619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12605.77 seconds wall clock time: 215 minutes 49.14 seconds (12949.14 seconds total)